scbi_blast 0.0.32 → 0.0.33
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- data/History.txt +4 -0
- data/lib/scbi_blast/batch_blast.rb +23 -16
- data/lib/scbi_blast.rb +1 -1
- metadata +2 -2
data/History.txt
CHANGED
@@ -60,22 +60,9 @@ class BatchBlast
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end
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cmd = get_blast_cmd(fmt)
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63
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-
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-
res=
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-
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-
# Ojo, que una vez nos ibamos a volver locos buscando porque esto no devolvia todos los hits que se encontraban al ejecutar el blast a mano, y era porque en el blast a mano le estabamos pasando la secuencia completa mientras que en el MID le estabamos pasando solo los 20 primeros nt.
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-
IO.popen(cmd,'w+') {|blast|
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-
blast.sync = true
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-
blast.write(seq_fasta)
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-
blast.close_write
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-
res = blast.readlines
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-
blast.close_read
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-
}
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-
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-
if !$?.exitstatus.nil? && $?.exitstatus>0
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raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
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-
end
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-
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+
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res = BatchBlast.do_blast_cmd(seq_fasta,cmd)
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+
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# check if all sequences where processed
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if parse_output
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if fmt == :table
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@@ -101,6 +88,26 @@ class BatchBlast
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end
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end
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+
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return res
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+
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end
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+
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def self.do_blast_cmd(seq_fasta, cmd)
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res=''
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+
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# Ojo, que una vez nos ibamos a volver locos buscando porque esto no devolvia todos los hits que se encontraban al ejecutar el blast a mano, y era porque en el blast a mano le estabamos pasando la secuencia completa mientras que en el MID le estabamos pasando solo los 20 primeros nt.
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IO.popen(cmd,'w+') {|blast|
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blast.sync = true
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blast.write(seq_fasta)
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blast.close_write
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res = blast.readlines
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blast.close_read
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}
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if !$?.exitstatus.nil? && $?.exitstatus>0
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raise "Error doing blast #{cmd} to fasta: #{seq_fasta}"
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end
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return res
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data/lib/scbi_blast.rb
CHANGED
metadata
CHANGED
@@ -2,7 +2,7 @@
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name: scbi_blast
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version: !ruby/object:Gem::Version
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prerelease:
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-
version: 0.0.
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+
version: 0.0.33
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platform: ruby
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authors:
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- Dario Guerrero & Almudena Bocinos
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@@ -10,7 +10,7 @@ autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2011-06
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+
date: 2011-07-06 00:00:00 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: hoe
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